WO2015193483A1 - Réactions en chaîne par polymérase quantitatives médiées par restriction - Google Patents

Réactions en chaîne par polymérase quantitatives médiées par restriction Download PDF

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Publication number
WO2015193483A1
WO2015193483A1 PCT/EP2015/063832 EP2015063832W WO2015193483A1 WO 2015193483 A1 WO2015193483 A1 WO 2015193483A1 EP 2015063832 W EP2015063832 W EP 2015063832W WO 2015193483 A1 WO2015193483 A1 WO 2015193483A1
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WIPO (PCT)
Prior art keywords
pcr
polymerase chain
nucleic acid
chain reaction
acid sequence
Prior art date
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PCT/EP2015/063832
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English (en)
Inventor
Jurgen DEL FAVERO
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Multiplicom N.V.
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Publication date
Application filed by Multiplicom N.V. filed Critical Multiplicom N.V.
Priority to US15/319,279 priority Critical patent/US10947588B2/en
Priority to EP15730159.9A priority patent/EP3158082B1/fr
Publication of WO2015193483A1 publication Critical patent/WO2015193483A1/fr
Priority to US17/172,540 priority patent/US11926870B2/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/686—Polymerase chain reaction [PCR]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6851—Quantitative amplification
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6818—Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/131—Modifications characterised by incorporating a restriction site
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/30—Oligonucleotides characterised by their secondary structure
    • C12Q2525/301—Hairpin oligonucleotides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/143—Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2561/00—Nucleic acid detection characterised by assay method
    • C12Q2561/113—Real time assay
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/10—Detection mode being characterised by the assay principle
    • C12Q2565/101—Interaction between at least two labels

Definitions

  • the present invention relates to the technical field of nucleic acid amplification using a Polymerase Chain Reaction (PCR). Specifically, the present invention relates to
  • PCR Polymerase Chain Reaction
  • PCR Polymerase Chain Reaction
  • PCR Polymerase Chain Reaction
  • qPCR quantitative Polymerase Chain Reaction
  • qPCR quantitative polymerase chain reaction
  • PCR polymerase chain reaction
  • a polymerase chain reaction generally consists of series of repeated, for example 15 to 60 times, cycles of temperature changes. These temperature cycles generally comprise at least three stages: the first stage, at around 95 °C, allows for separation of the nucleic acid's double chain; the second stage, at a temperature of around 45 to 65°C, allows for binding of primers with a DNA template and the third stage, at between 68 to 75 °C, facilitates polymerization carried out by a DNA polymerase thereby providing amplification of a target nucleic acid sequence.
  • the specific temperatures and the time intervals used in each cycle depend on a number of parameters, such as enzymes used to duplicate the target DNA, concentration of divalent ions and deoxyribonucleotides (dNTPs) and annealing temperatures of the primers used.
  • enzymes used to duplicate the target DNA concentration of divalent ions and deoxyribonucleotides (dNTPs) and annealing temperatures of the primers used.
  • dNTPs deoxyribonucleotides
  • a quantitative polymerase chain reaction is generally used to amplify, and quantify, a targeted DNA molecule.
  • quantitative PCR enables both detection and quantification.
  • the quantity can be either an absolute number of copies or a relative amount when the amplification products are normalized to DNA input or reference genes.
  • Quantitative PCR is generally carried out in a thermal cycler with the capacity to illuminate each sample with a beam of light of a specified wavelength and to detect the fluorescence emitted by the excited chromo- or fluorophore.
  • Multiplex polymerase chain reaction is a modification of polymerase chain reaction.
  • a multiplex polymerase chain reaction uses two or more primer sets within a single PCR mixture to produce amplicons that are specific to different DNA sequences. By pursuing multiple targets at once, additional information may be gained from a single test run otherwise requiring several separate PCR reactions.
  • qPCR quantitative polymerase chain reaction
  • multiplex polymerase chain reaction multiplex PCR
  • qPCR quantitative polymerase chain reaction
  • multiplex PCR multiplex polymerase chain reaction
  • the above object of the present invention is met by the present invention by a novel PCR assay as outlined below and in the appended claims.
  • the presnt novel PCR assay is designated herein as RM-QPCR or Restriction Mediated Quantitative PCR.
  • PCR Polymerase Chain Reaction
  • RM-qPCR Restriction Mediated quantitative PCR
  • 5' Acceptor represents one member of a fluorescence resonance energy transfer (FRET) pair
  • A represents a nucleic acid sequence motif of 10 to 30 bp
  • 3-C represents a linker region comprised of at least three carbon atoms
  • B represents a double stranded restriction enzyme recognition site or a random
  • A' represents a nucleic acid sequence motif of 10 to 30 bp being complementary to the nucleic acid sequence motif of A
  • R-prim represents a nucleic acid sequence complementary to a target sequence in a nucleic acid sequence to be amplified.
  • FRET fluorescence resonance energy transfer
  • FRET Forster resonance energy transfer
  • FRET fluorescence resonance energy transfer
  • RET resonance energy transfer
  • EET electronic energy transfer
  • the present double stranded restriction enzyme recognition site B is a 5 to 15 bp PspGl restriction enzyme recognition sequence.
  • PspGl is a restriction enzyme recognizing and cleaving the dsDNA sequence: 'CCWGG/GGWCC' .
  • the enzyme's optimal temperature is 75°C and the enzyme is resistant to heat inactivation and, accordingly, is especially suitable to be used according to the present invention.
  • PspGl like restriction enzymes or genome editing nuclease tools such as CRISPR, CAS9, Talen and ZFN or engineered hybrid
  • RNase H based cleavage at the B - sequence can be envisaged by incorporating a RNA base at a specific B position of the R-prim based primer which can be cleaved, during the QPCR, by a thermostable RNase H based on the nature of RNaseH to cut at a RNA base in case of a perfect sequence similarity.
  • the present invention relates to Polymerase Chain Reaction (PCR) nucleic acid amplification mixtures comprising:
  • PCR Polymerase Chain Reaction
  • 5' Donor represents one member of a fluorescence resonance energy transfer (FRET) pair comprised of a light emitting molecule
  • A' represents a nucleic acid sequence motif of 10 to 30 bp being complementary to the nucleic acid sequence motif of A;
  • restriction enzyme preferably PspGl ;
  • a detectable signal is obtained after cleavage of the restriction site B and a subsequent hybridization as is graphically depicted in Figure 3.
  • PCR Polymerase Chain Reaction
  • FRET fluorescence resonance energy transfer
  • the present invention relates to the use of the present Polymerase Chain Reaction (PCR) primers or the present Polymerase Chain Reaction (PCR) nucleic acid amplification mixtures in a Polymerase Chain Reaction (PCR), preferably a quantitative Polymerase Chain Reaction (qPCR).
  • PCR Polymerase Chain Reaction
  • qPCR quantitative Polymerase Chain Reaction
  • the present use according this aspect of the invention allows for the amplification of at least 4, preferably at least 6, more preferably at least 10 amplicons in a single nucleic acid amplification reaction such as 4, 5, 6, 7, 8, ,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, or 39 amplicons.
  • Figure 1 graphical representation of the general structure of an amplification primer
  • FIG. 2 graphical representation of the general structure of a fluorophore donor probe according to the present invention
  • the RM-QPCR is short for Restriction Mediated Quantitative PCR and is developed to realize the unmet need of highly multiplexed QPCR assays.
  • Current QPCR methods using standard equipment only allow limited multiplexing of up to 2 or 3 amplicons per reaction. With RM-QPCR it is theoretically possible to derive multiplexes of up to 30-40 amplicons per reaction.
  • Each target amplicon is amplified by using a standard PCR primer (S-prim: 18-27 bp in length) and the present primer (R-prim: 70-80 bp in length: Figure 1) composed of the following elements (from 3' to 5'):
  • Amplicon specific sequence that in combination with the standard PCR primer will drive amplification if template DNA is present (R-prim).
  • A' sequence motif ( ⁇ 20 bp) which is complementary to the A sequence motif.
  • PspGl is a restriction enzyme recognising and cleaving the dsDNA sequence: 'CCWGG/GGWCC
  • the enzymes optimal temperature is 75°C and the enzyme resistant to heat inactivation and hence can be used in a PCR reaction.
  • a sequence motif ( ⁇ 20 bp) which is complementary to the A' sequence which contains a covalently attached fluorescent label (e.g. ROX)
  • a PCR reaction is set-up containing the following components:
  • the donor oligonucleotide has the sequence A' and hence is
  • the PspGl mediated release of the A sequence motif will result in hybridisation with the donor oligonucleotide allowing detection of amplification by FRET (Fluorescence Resonance Energy Transfer) by close proximity of the fluorescent label from the A sequence motif (acceptor) and the fluorescent label on the donor oligonucleotide
  • FRET Fluorescence Resonance Energy Transfer
  • FRET will only occur if the single stranded A sequence motif is physically removed from R- prim.
  • Multiplexing can be achieved by:

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
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  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
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  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

La présente invention concerne le domaine technique de l'amplification des acides nucléiques à l'aide d'une réaction en chaîne par polymérase (PCR). Plus précisément, la présente invention concerne des amorces de réaction en chaîne par polymérase (PCR) et un mélange pour l'amplification d'acide nucléique par réaction en chaîne par polymérase (PCR) et leur utilisation dans des réactions en chaîne par polymérase (PCR) (quantitatives). Plus précisément, la présente invention concerne des amorces de réaction en chaîne par polymérase (PCR) appropriées pour une utilisation dans des réactions d'amplification d'acide nucléique de type PCR quantitative médiée par restriction (RM-qPCR) comprenant un accepteur en 5' (5' Accepteur) représentant un élément d'une paire de transfert d'énergie de fluorescence par résonance (FRET); A représentant un motif de séquence d'acide nucléique de 10 à 30 pb; 3-C représentant une région de liaison constituée d'au moins trois atomes de carbone; B représentant un site de reconnaissance d'enzyme de restriction double brin ou une séquence d'acide nucléique aléatoire; A' représentant un motif de séquence d'acide nucléique de 10 à 30 pb étant complémentaire du motif de séquence d'acide nucléique de A; et R-prim représentant une séquence d'acide nucléique complémentaire d'une séquence cible dans une séquence d'acide nucléique qui doit être amplifiée.
PCT/EP2015/063832 2014-06-19 2015-06-19 Réactions en chaîne par polymérase quantitatives médiées par restriction WO2015193483A1 (fr)

Priority Applications (3)

Application Number Priority Date Filing Date Title
US15/319,279 US10947588B2 (en) 2014-06-19 2015-06-19 Restriction mediated quantitative polymerase chain reactions
EP15730159.9A EP3158082B1 (fr) 2014-06-19 2015-06-19 Réactions en chaîne par polymérase quantitatives médiées par restriction
US17/172,540 US11926870B2 (en) 2014-06-19 2021-02-10 Restriction mediated quantitative polymerase chain reactions

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EPPCT/EP2014/062971 2014-06-19
EP2014062971 2014-06-19

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US15/319,279 A-371-Of-International US10947588B2 (en) 2014-06-19 2015-06-19 Restriction mediated quantitative polymerase chain reactions
US17/172,540 Continuation US11926870B2 (en) 2014-06-19 2021-02-10 Restriction mediated quantitative polymerase chain reactions

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Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3158082B1 (fr) * 2014-06-19 2020-12-30 Multiplicom NV Réactions en chaîne par polymérase quantitatives médiées par restriction

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001038570A1 (fr) * 1999-11-29 2001-05-31 Gamida Sense Diagnostics Ltd. Oligonucleotides et assemblages d'oligonucleotides convenant a la confirmation d'absence ou de presence de sequences d'acides nucleiques cibles dans un echantillon
WO2010139937A1 (fr) * 2009-06-01 2010-12-09 Oxitec Limited Amplification multiplexe et détection
WO2011063388A2 (fr) * 2009-11-23 2011-05-26 Becton, Dickinson And Company Procédé de dosage pour un acide nucléique cible par amplification de signal à l'aide d'hybridation et de restriction de sondes
WO2011141738A1 (fr) * 2010-05-11 2011-11-17 Enigma Diagnostics Limited Système de signalisation
WO2012024639A1 (fr) * 2010-08-20 2012-02-23 Life Technologies Corporation Dosage de polymérase avec un substrat de transfert d'énergie par résonance de fluorescence

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090068643A1 (en) * 2005-11-23 2009-03-12 Integrated Dna Technologies, Inc. Dual Function Primers for Amplifying DNA and Methods of Use
US8008019B2 (en) * 2007-11-28 2011-08-30 Luminex Molecular Diagnostics Use of dual-tags for the evaluation of genomic variable repeat regions
JP5785942B2 (ja) * 2009-06-29 2015-09-30 ルミネックス コーポレーション ヘアピンコンフォメーションを有するキメラプライマーおよびその使用法
EP3158082B1 (fr) * 2014-06-19 2020-12-30 Multiplicom NV Réactions en chaîne par polymérase quantitatives médiées par restriction

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001038570A1 (fr) * 1999-11-29 2001-05-31 Gamida Sense Diagnostics Ltd. Oligonucleotides et assemblages d'oligonucleotides convenant a la confirmation d'absence ou de presence de sequences d'acides nucleiques cibles dans un echantillon
WO2010139937A1 (fr) * 2009-06-01 2010-12-09 Oxitec Limited Amplification multiplexe et détection
WO2011063388A2 (fr) * 2009-11-23 2011-05-26 Becton, Dickinson And Company Procédé de dosage pour un acide nucléique cible par amplification de signal à l'aide d'hybridation et de restriction de sondes
WO2011141738A1 (fr) * 2010-05-11 2011-11-17 Enigma Diagnostics Limited Système de signalisation
WO2012024639A1 (fr) * 2010-08-20 2012-02-23 Life Technologies Corporation Dosage de polymérase avec un substrat de transfert d'énergie par résonance de fluorescence

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
SOLINAS A ET AL: "Duplex Scorpion primers in SNP analysis and FRET applications", NUCLEIC ACIDS RESEARCH, INFORMATION RETRIEVAL LTD, vol. 29, no. 20, 15 October 2001 (2001-10-15), pages E96, XP002318909, ISSN: 0305-1048, DOI: 10.1093/NAR/29.20.E96 *

Also Published As

Publication number Publication date
EP3158082B1 (fr) 2020-12-30
US20210269853A1 (en) 2021-09-02
EP3158082A1 (fr) 2017-04-26
US20170137865A1 (en) 2017-05-18
US10947588B2 (en) 2021-03-16
US11926870B2 (en) 2024-03-12

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